{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Juvenile\" and tissue_curation = \"Eye\"", "rows": [[42042, "SRR5382042", "SRX2677135", "SRS2075556", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. 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This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf sclera 13", "GSM2552012", null, "tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf sclera 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. 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ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf sclera 12", "GSM2552011", null, "tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf sclera 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. 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ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf sclera 12", "GSM2552011", null, "tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf sclera 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. 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ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf sclera 11", "GSM2552010", null, "tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf sclera 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. 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ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf sclera 11", "GSM2552010", null, "tissue:choroid/sclera|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf sclera 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. 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ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 13", "GSM2552009", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. 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RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552009", "GSM2552009: lrp2 mpf 1 mpf retina 13; Danio rerio; RNA Seq", "GSM2552009", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552009", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAWRAAPEI-201_1.fq.gz", "fastq", 754821823.0, 15404527.0, "GSM2552009 r1", "0:49 1:0", "A:206101700;C:172880224;G:168016286;T:207817318;N:6295", 49, 0, null, null, 206101700, 172880224, 168016286, 207817318, 6295, "SRX2677132", "SRS2075553", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88663, null, 0.1569, null, 0.70934, null, 0.50146, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42049, "SRR5382037", "SRX2677132", "SRS2075553", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 13", "GSM2552009", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552009", "GSM2552009: lrp2 mpf 1 mpf retina 13; Danio rerio; RNA Seq", "GSM2552009", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552009", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAWRAAPEI-201_1.fq.gz", "fastq", 738593856.0, 15073344.0, "GSM2552009 r2", "0:49 1:0", "A:201412233;C:169280089;G:164643585;T:203250732;N:7217", 49, 0, null, null, 201412233, 169280089, 164643585, 203250732, 7217, "SRX2677132", "SRS2075553", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89286, null, 0.15576, null, 0.70707, null, 0.50361, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42050, "SRR5382034", "SRX2677131", "SRS2075552", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 12", "GSM2552008", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552008", "GSM2552008: lrp2 mpf 1 mpf retina 12; Danio rerio; RNA Seq", "GSM2552008", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552008", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAVRAAPEI-227_1.fq.gz", "fastq", 905999220.0, 18489780.0, "GSM2552008 r1", "0:49 1:0", "A:247171602;C:207706839;G:201939609;T:249173819;N:7351", 49, 0, null, null, 247171602, 207706839, 201939609, 249173819, 7351, "SRX2677131", "SRS2075552", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88857, null, 0.16101, null, 0.70634, null, 0.49492, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42051, "SRR5382035", "SRX2677131", "SRS2075552", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 12", "GSM2552008", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552008", "GSM2552008: lrp2 mpf 1 mpf retina 12; Danio rerio; RNA Seq", "GSM2552008", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552008", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAVRAAPEI-227_1.fq.gz", "fastq", 898471938.0, 18336162.0, "GSM2552008 r2", "0:49 1:0", "A:244766986;C:206211428;G:200463923;T:247021077;N:8524", 49, 0, null, null, 244766986, 206211428, 200463923, 247021077, 8524, "SRX2677131", "SRS2075552", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89516, null, 0.16388, null, 0.7064, null, 0.4955, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42052, "SRR5382032", "SRX2677130", "SRS2075551", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 11", "GSM2552007", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552007", "GSM2552007: lrp2 mpf 1 mpf retina 11; Danio rerio; RNA Seq", "GSM2552007", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552007", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L6_HKZEBxagRAAURAAPEI-225_1.fq.gz", "fastq", 821148272.0, 16758128.0, "GSM2552007 r1", "0:49 1:0", "A:223278809;C:188723305;G:184465552;T:224674360;N:6246", 49, 0, null, null, 223278809, 188723305, 184465552, 224674360, 6246, "SRX2677130", "SRS2075551", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89197, null, 0.15625, null, 0.70502, null, 0.48945, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42053, "SRR5382033", "SRX2677130", "SRS2075551", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf retina 11", "GSM2552007", null, "tissue:retina|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf retina 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552007", "GSM2552007: lrp2 mpf 1 mpf retina 11; Danio rerio; RNA Seq", "GSM2552007", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552007", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L7_HKZEBxagRAAURAAPEI-225_1.fq.gz", "fastq", 904858500.0, 18466500.0, "GSM2552007 r2", "0:49 1:0", "A:245787210;C:208119300;G:203490934;T:247452637;N:8419", 49, 0, null, null, 245787210, 208119300, 203490934, 247452637, 8419, "SRX2677130", "SRS2075551", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89893, null, 0.15664, null, 0.70382, null, 0.49338, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42054, "SRR5382031", "SRX2677129", "SRS2075550", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf RPE 21", "GSM2552006", null, "tissue:retinal pigment epithelium|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf RPE 21", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552006", "GSM2552006: lrp2 mpf 1 mpf RPE 21; Danio rerio; RNA Seq", "GSM2552006", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552006", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150726_I114_FCH35J7BBXX_L7_HKZEBxagRBAARABPEI-220_1.fq.gz", "fastq", 1640688315.0, 33483435.0, "GSM2552006 r1", "0:49 1:0", "A:433572086;C:384856932;G:377705367;T:444542626;N:11304", 49, 0, null, null, 433572086, 384856932, 377705367, 444542626, 11304, "SRX2677129", "SRS2075550", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.894, null, 0.12185, null, 0.68781, null, 0.49822, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42055, "SRR5382029", "SRX2677128", "SRS2075549", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf RPE 13", "GSM2552005", null, "tissue:retinal pigment epithelium|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf RPE 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552005", "GSM2552005: lrp2 mpf 1 mpf RPE 13; Danio rerio; RNA Seq", "GSM2552005", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552005", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAQRAAPEI-220_1.fq.gz", "fastq", 676224157.0, 13800493.0, "GSM2552005 r1", "0:49 1:0", "A:180366332;C:156589454;G:154935435;T:182635962;N:1696974", 49, 0, null, null, 180366332, 156589454, 154935435, 182635962, 1696974, "SRX2677128", "SRS2075549", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89751, null, 0.13119, null, 0.69441, null, 0.50128, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42056, "SRR5382030", "SRX2677128", "SRS2075549", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf RPE 13", "GSM2552005", null, "tissue:retinal pigment epithelium|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf RPE 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552005", "GSM2552005: lrp2 mpf 1 mpf RPE 13; Danio rerio; RNA Seq", "GSM2552005", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552005", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAQRAAPEI-220_1.fq.gz", "fastq", 801242267.0, 16351883.0, "GSM2552005 r2", "0:49 1:0", "A:214063611;C:186150617;G:184165214;T:216859021;N:3804", 49, 0, null, null, 214063611, 186150617, 184165214, 216859021, 3804, "SRX2677128", "SRS2075549", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.9008, null, 0.13185, null, 0.69323, null, 0.4968, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42057, "SRR5382027", "SRX2677127", "SRS2075548", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf RPE 12", "GSM2552004", null, "tissue:retinal pigment epithelium|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf RPE 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552004", "GSM2552004: lrp2 mpf 1 mpf RPE 12; Danio rerio; RNA Seq", "GSM2552004", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552004", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAPRAAPEI-219_1.fq.gz", "fastq", 661637837.0, 13502813.0, "GSM2552004 r1", "0:49 1:0", "A:176324364;C:153911375;G:151275995;T:178389637;N:1736466", 49, 0, null, null, 176324364, 153911375, 151275995, 178389637, 1736466, "SRX2677127", "SRS2075548", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89679, null, 0.12464, null, 0.68205, null, 0.49183, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42058, "SRR5382028", "SRX2677127", "SRS2075548", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf RPE 12", "GSM2552004", null, "tissue:retinal pigment epithelium|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf RPE 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552004", "GSM2552004: lrp2 mpf 1 mpf RPE 12; Danio rerio; RNA Seq", "GSM2552004", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552004", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAPRAAPEI-219_1.fq.gz", "fastq", 771285088.0, 15740512.0, "GSM2552004 r2", "0:49 1:0", "A:205889481;C:180075876;G:176967027;T:208349042;N:3662", 49, 0, null, null, 205889481, 180075876, 176967027, 208349042, 3662, "SRX2677127", "SRS2075548", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89897, null, 0.12535, null, 0.68337, null, 0.48697, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42059, "SRR5382025", "SRX2677126", "SRS2075547", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 3", "GSM2552003", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 3", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552003", "GSM2552003: lrp2 mpf 1 mpf eyes 3; Danio rerio; RNA Seq", "GSM2552003", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552003", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAORAAPEI-218_1.fq.gz", "fastq", 723477454.0, 14764846.0, "GSM2552003 r1", "0:49 1:0", "A:192239117;C:170175036;G:165348255;T:193868733;N:1846313", 49, 0, null, null, 192239117, 170175036, 165348255, 193868733, 1846313, "SRX2677126", "SRS2075547", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90222, null, 0.12773, null, 0.68617, null, 0.47685, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42060, "SRR5382026", "SRX2677126", "SRS2075547", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 3", "GSM2552003", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 3", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552003", "GSM2552003: lrp2 mpf 1 mpf eyes 3; Danio rerio; RNA Seq", "GSM2552003", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552003", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAORAAPEI-218_1.fq.gz", "fastq", 849657746.0, 17339954.0, "GSM2552003 r2", "0:49 1:0", "A:226120997;C:200571753;G:194784071;T:228176838;N:4087", 49, 0, null, null, 226120997, 200571753, 194784071, 228176838, 4087, "SRX2677126", "SRS2075547", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90381, null, 0.12659, null, 0.68527, null, 0.47307, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42061, "SRR5382023", "SRX2677125", "SRS2075546", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 2", "GSM2552002", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 2", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552002", "GSM2552002: lrp2 mpf 1 mpf eyes 2; Danio rerio; RNA Seq", "GSM2552002", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552002", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAANRAAPEI-216_1.fq.gz", "fastq", 731986010.0, 14938490.0, "GSM2552002 r1", "0:49 1:0", "A:194148078;C:172782798;G:168124540;T:195035708;N:1894886", 49, 0, null, null, 194148078, 172782798, 168124540, 195035708, 1894886, "SRX2677125", "SRS2075546", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90549, null, 0.10568, null, 0.6884, null, 0.476, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42062, "SRR5382024", "SRX2677125", "SRS2075546", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 2", "GSM2552002", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 2", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552002", "GSM2552002: lrp2 mpf 1 mpf eyes 2; Danio rerio; RNA Seq", "GSM2552002", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552002", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAANRAAPEI-216_1.fq.gz", "fastq", 862250991.0, 17596959.0, "GSM2552002 r2", "0:49 1:0", "A:229099692;C:204203154;G:198695417;T:230248629;N:4099", 49, 0, null, null, 229099692, 204203154, 198695417, 230248629, 4099, "SRX2677125", "SRS2075546", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90837, null, 0.10601, null, 0.68903, null, 0.45932, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42063, "SRR5382021", "SRX2677124", "SRS2075545", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 1", "GSM2552001", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 1", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552001", "GSM2552001: lrp2 mpf 1 mpf eyes 1; Danio rerio; RNA Seq", "GSM2552001", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552001", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAMRAAPEI-214_1.fq.gz", "fastq", 869975253.0, 17754597.0, "GSM2552001 r1", "0:49 1:0", "A:229664008;C:206113797;G:200906294;T:231030590;N:2260564", 49, 0, null, null, 229664008, 206113797, 200906294, 231030590, 2260564, "SRX2677124", "SRS2075545", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90483, null, 0.11515, null, 0.68515, null, 0.47313, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42064, "SRR5382022", "SRX2677124", "SRS2075545", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "lrp2 mpf 1 mpf eyes 1", "GSM2552001", null, "tissue:whole eyes|genotype:lrp2 / |age:1 mpf", "lrp2 mpf 1 mpf eyes 1", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:lrp2 / |age:1 mpf", "GSM2552001", "GSM2552001: lrp2 mpf 1 mpf eyes 1; Danio rerio; RNA Seq", "GSM2552001", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552001", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAMRAAPEI-214_1.fq.gz", "fastq", 914727884.0, 18667916.0, "GSM2552001 r2", "0:49 1:0", "A:241918752;C:217461160;G:211918468;T:243425755;N:3749", 49, 0, null, null, 241918752, 217461160, 211918468, 243425755, 3749, "SRX2677124", "SRS2075545", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.90759, null, 0.11592, null, 0.68505, null, 0.48054, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42065, "SRR5382019", "SRX2677123", "SRS2075544", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 13", "GSM2552000", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2552000", "GSM2552000: ZDR 1 mpf sclera 13; Danio rerio; RNA Seq", "GSM2552000", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552000", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAIRAAPEI-210_1.fq.gz", "fastq", 723705892.0, 14769508.0, "GSM2552000 r1", "0:49 1:0", "A:189459230;C:171808598;G:168845608;T:191709984;N:1882472", 49, 0, null, null, 189459230, 171808598, 168845608, 191709984, 1882472, "SRX2677123", "SRS2075544", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.8885, null, 0.08592, null, 0.7093, null, 0.46515, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42066, "SRR5382020", "SRX2677123", "SRS2075544", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 13", "GSM2552000", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2552000", "GSM2552000: ZDR 1 mpf sclera 13; Danio rerio; RNA Seq", "GSM2552000", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2552000", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAIRAAPEI-210_1.fq.gz", "fastq", 835178687.0, 17044463.0, "GSM2552000 r2", "0:49 1:0", "A:219032897;C:198915529;G:195473137;T:221752813;N:4311", 49, 0, null, null, 219032897, 198915529, 195473137, 221752813, 4311, "SRX2677123", "SRS2075544", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89282, null, 0.08675, null, 0.70767, null, 0.46691, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42067, "SRR5382017", "SRX2677122", "SRS2075543", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 12", "GSM2551999", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551999", "GSM2551999: ZDR 1 mpf sclera 12; Danio rerio; RNA Seq", "GSM2551999", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551999", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAHRAAPEI-209_1.fq.gz", "fastq", 720619774.0, 14706526.0, "GSM2551999 r1", "0:49 1:0", "A:189843421;C:170258398;G:165954852;T:192642877;N:1920226", 49, 0, null, null, 189843421, 170258398, 165954852, 192642877, 1920226, "SRX2677122", "SRS2075543", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88799, null, 0.09077, null, 0.69307, null, 0.46834, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42068, "SRR5382018", "SRX2677122", "SRS2075543", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 12", "GSM2551999", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551999", "GSM2551999: ZDR 1 mpf sclera 12; Danio rerio; RNA Seq", "GSM2551999", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551999", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAHRAAPEI-209_1.fq.gz", "fastq", 814612652.0, 16624748.0, "GSM2551999 r2", "0:49 1:0", "A:215000926;C:193099554;G:188185253;T:218322960;N:3959", 49, 0, null, null, 215000926, 193099554, 188185253, 218322960, 3959, "SRX2677122", "SRS2075543", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89194, null, 0.09267, null, 0.69345, null, 0.47187, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42069, "SRR5382015", "SRX2677121", "SRS2075542", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 11", "GSM2551998", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551998", "GSM2551998: ZDR 1 mpf sclera 11; Danio rerio; RNA Seq", "GSM2551998", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAGRAAPEI-208_1.fq.gz", "fastq", 711301150.0, 14516350.0, "GSM2551998 r1", "0:49 1:0", "A:187610754;C:167656660;G:164414397;T:189785378;N:1833961", 49, 0, null, null, 187610754, 167656660, 164414397, 189785378, 1833961, "SRX2677121", "SRS2075542", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89019, null, 0.08546, null, 0.71112, null, 0.46026, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42070, "SRR5382016", "SRX2677121", "SRS2075542", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf sclera 11", "GSM2551998", null, "tissue:choroid/sclera|genotype:wild type|age:1 mpf", "ZDR 1 mpf sclera 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "choroid/sclera", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551998", "GSM2551998: ZDR 1 mpf sclera 11; Danio rerio; RNA Seq", "GSM2551998", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551998", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAGRAAPEI-208_1.fq.gz", "fastq", 812115073.0, 16573777.0, "GSM2551998 r2", "0:49 1:0", "A:214551124;C:192083365;G:188317025;T:217159406;N:4153", 49, 0, null, null, 214551124, 192083365, 188317025, 217159406, 4153, "SRX2677121", "SRS2075542", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89273, null, 0.08561, null, 0.71151, null, 0.46434, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42071, "SRR5382013", "SRX2677120", "SRS2075541", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 13", "GSM2551997", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551997", "GSM2551997: ZDR 1 mpf retina 13; Danio rerio; RNA Seq", "GSM2551997", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551997", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAALRAAPEI-213_1.fq.gz", "fastq", 627516148.0, 12806452.0, "GSM2551997 r1", "0:49 1:0", "A:170179227;C:144206894;G:141003173;T:170495840;N:1631014", 49, 0, null, null, 170179227, 144206894, 141003173, 170495840, 1631014, "SRX2677120", "SRS2075541", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.87699, null, 0.15658, null, 0.70853, null, 0.4864, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42072, "SRR5382014", "SRX2677120", "SRS2075541", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 13", "GSM2551997", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551997", "GSM2551997: ZDR 1 mpf retina 13; Danio rerio; RNA Seq", "GSM2551997", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551997", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAALRAAPEI-213_1.fq.gz", "fastq", 728730597.0, 14872053.0, "GSM2551997 r2", "0:49 1:0", "A:197954872;C:168023610;G:164244521;T:198504024;N:3570", 49, 0, null, null, 197954872, 168023610, 164244521, 198504024, 3570, "SRX2677120", "SRS2075541", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88024, null, 0.15744, null, 0.70798, null, 0.4864, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42073, "SRR5382011", "SRX2677119", "SRS2075540", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 12", "GSM2551996", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551996", "GSM2551996: ZDR 1 mpf retina 12; Danio rerio; RNA Seq", "GSM2551996", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551996", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAKRAAPEI-212_1.fq.gz", "fastq", 750179269.0, 15309781.0, "GSM2551996 r1", "0:49 1:0", "A:202189760;C:173630838;G:168978527;T:203409292;N:1970852", 49, 0, null, null, 202189760, 173630838, 168978527, 203409292, 1970852, "SRX2677119", "SRS2075540", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88077, null, 0.14126, null, 0.70589, null, 0.49134, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42074, "SRR5382012", "SRX2677119", "SRS2075540", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 12", "GSM2551996", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551996", "GSM2551996: ZDR 1 mpf retina 12; Danio rerio; RNA Seq", "GSM2551996", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551996", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAKRAAPEI-212_1.fq.gz", "fastq", 897558088.0, 18317512.0, "GSM2551996 r2", "0:49 1:0", "A:242294855;C:208492061;G:202846754;T:243920033;N:4385", 49, 0, null, null, 242294855, 208492061, 202846754, 243920033, 4385, "SRX2677119", "SRS2075540", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.8857, null, 0.14195, null, 0.70536, null, 0.48882, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42075, "SRR5382009", "SRX2677118", "SRS2075539", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 11", "GSM2551995", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551995", "GSM2551995: ZDR 1 mpf retina 11; Danio rerio; RNA Seq", "GSM2551995", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551995", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAJRAAPEI-211_1.fq.gz", "fastq", 823785942.0, 16811958.0, "GSM2551995 r1", "0:49 1:0", "A:222797674;C:189722377;G:184455267;T:224717827;N:2092797", 49, 0, null, null, 222797674, 189722377, 184455267, 224717827, 2092797, "SRX2677118", "SRS2075539", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.87839, null, 0.15243, null, 0.70987, null, 0.49087, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42076, "SRR5382010", "SRX2677118", "SRS2075539", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf retina 11", "GSM2551995", null, "tissue:retina|genotype:wild type|age:1 mpf", "ZDR 1 mpf retina 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retina", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551995", "GSM2551995: ZDR 1 mpf retina 11; Danio rerio; RNA Seq", "GSM2551995", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551995", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAJRAAPEI-211_1.fq.gz", "fastq", 915019826.0, 18673874.0, "GSM2551995 r2", "0:49 1:0", "A:247862749;C:211485352;G:205487891;T:250180081;N:3753", 49, 0, null, null, 247862749, 211485352, 205487891, 250180081, 3753, "SRX2677118", "SRS2075539", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88022, null, 0.1533, null, 0.71023, null, 0.4871, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42077, "SRR5382007", "SRX2677117", "SRS2075538", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 13", "GSM2551994", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551994", "GSM2551994: ZDR 1 mpf RPE 13; Danio rerio; RNA Seq", "GSM2551994", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAFRAAPEI-207_1.fq.gz", "fastq", 638481025.0, 13030225.0, "GSM2551994 r1", "0:49 1:0", "A:169350435;C:149047615;G:147980872;T:170459893;N:1642210", 49, 0, null, null, 169350435, 149047615, 147980872, 170459893, 1642210, "SRX2677117", "SRS2075538", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89027, null, 0.11552, null, 0.69268, null, 0.47791, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42078, "SRR5382008", "SRX2677117", "SRS2075538", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 13", "GSM2551994", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 13", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551994", "GSM2551994: ZDR 1 mpf RPE 13; Danio rerio; RNA Seq", "GSM2551994", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551994", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAFRAAPEI-207_1.fq.gz", "fastq", 753109420.0, 15369580.0, "GSM2551994 r2", "0:49 1:0", "A:200026171;C:176448366;G:175132341;T:201498888;N:3654", 49, 0, null, null, 200026171, 176448366, 175132341, 201498888, 3654, "SRX2677117", "SRS2075538", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89342, null, 0.1153, null, 0.69301, null, 0.47451, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42079, "SRR5382005", "SRX2677116", "SRS2075537", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 12", "GSM2551993", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551993", "GSM2551993: ZDR 1 mpf RPE 12; Danio rerio; RNA Seq", "GSM2551993", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAERAAPEI-206_1.fq.gz", "fastq", 711158756.0, 14513444.0, "GSM2551993 r1", "0:49 1:0", "A:190423173;C:164563930;G:162474409;T:191835770;N:1861474", 49, 0, null, null, 190423173, 164563930, 162474409, 191835770, 1861474, "SRX2677116", "SRS2075537", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88325, null, 0.12011, null, 0.69913, null, 0.49648, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42080, "SRR5382006", "SRX2677116", "SRS2075537", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 12", "GSM2551993", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 12", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551993", "GSM2551993: ZDR 1 mpf RPE 12; Danio rerio; RNA Seq", "GSM2551993", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551993", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAERAAPEI-206_1.fq.gz", "fastq", 822460884.0, 16784916.0, "GSM2551993 r2", "0:49 1:0", "A:220616018;C:191013675;G:188473709;T:222353408;N:4074", 49, 0, null, null, 220616018, 191013675, 188473709, 222353408, 4074, "SRX2677116", "SRS2075537", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88727, null, 0.11911, null, 0.69777, null, 0.48971, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42081, "SRR5382003", "SRX2677115", "SRS2075536", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 11", "GSM2551992", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551992", "GSM2551992: ZDR 1 mpf RPE 11; Danio rerio; RNA Seq", "GSM2551992", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAADRAAPEI-205_1.fq.gz", "fastq", 760825107.0, 15527043.0, "GSM2551992 r1", "0:49 1:0", "A:203332989;C:175754207;G:174105427;T:205609497;N:2022987", 49, 0, null, null, 203332989, 175754207, 174105427, 205609497, 2022987, "SRX2677115", "SRS2075536", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88248, null, 0.11721, null, 0.69398, null, 0.49648, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42082, "SRR5382004", "SRX2677115", "SRS2075536", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf RPE 11", "GSM2551992", null, "tissue:retinal pigment epithelium|genotype:wild type|age:1 mpf", "ZDR 1 mpf RPE 11", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "retinal pigment epithelium", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551992", "GSM2551992: ZDR 1 mpf RPE 11; Danio rerio; RNA Seq", "GSM2551992", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551992", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAADRAAPEI-205_1.fq.gz", "fastq", 839301057.0, 17128593.0, "GSM2551992 r2", "0:49 1:0", "A:224733625;C:194508202;G:192706180;T:227349310;N:3740", 49, 0, null, null, 224733625, 194508202, 192706180, 227349310, 3740, "SRX2677115", "SRS2075536", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.88552, null, 0.11818, null, 0.69392, null, 0.48632, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42083, "SRR5382001", "SRX2677114", "SRS2075535", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 3", "GSM2551991", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 3", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551991", "GSM2551991: ZDR 1 mpf eyes 3; Danio rerio; RNA Seq", "GSM2551991", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAACRAAPEI-203_1.fq.gz", "fastq", 736025815.0, 15020935.0, "GSM2551991 r1", "0:49 1:0", "A:196052955;C:172994773;G:168209012;T:196847875;N:1921200", 49, 0, null, null, 196052955, 172994773, 168209012, 196847875, 1921200, "SRX2677114", "SRS2075535", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89497, null, 0.11257, null, 0.68852, null, 0.47383, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42084, "SRR5382002", "SRX2677114", "SRS2075535", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 3", "GSM2551991", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 3", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551991", "GSM2551991: ZDR 1 mpf eyes 3; Danio rerio; RNA Seq", "GSM2551991", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551991", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAACRAAPEI-203_1.fq.gz", "fastq", 848026487.0, 17306663.0, "GSM2551991 r2", "0:49 1:0", "A:226256521;C:199987000;G:194486401;T:227292463;N:4102", 49, 0, null, null, 226256521, 199987000, 194486401, 227292463, 4102, "SRX2677114", "SRS2075535", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89861, null, 0.11296, null, 0.68836, null, 0.46508, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42085, "SRR5381999", "SRX2677113", "SRS2075534", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 2", "GSM2551990", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 2", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551990", "GSM2551990: ZDR 1 mpf eyes 2; Danio rerio; RNA Seq", "GSM2551990", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551990", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAABRAAPEI-202_1.fq.gz", "fastq", 802949770.0, 16386730.0, "GSM2551990 r1", "0:49 1:0", "A:213127526;C:188823533;G:184394258;T:214490681;N:2113772", 49, 0, null, null, 213127526, 188823533, 184394258, 214490681, 2113772, "SRX2677113", "SRS2075534", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89543, null, 0.10967, null, 0.69209, null, 0.47916, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42086, "SRR5382000", "SRX2677113", "SRS2075534", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 2", "GSM2551990", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 2", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551990", "GSM2551990: ZDR 1 mpf eyes 2; Danio rerio; RNA Seq", "GSM2551990", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551990", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAABRAAPEI-202_1.fq.gz", "fastq", 914629639.0, 18665911.0, "GSM2551990 r2", "0:49 1:0", "A:243198380;C:215821497;G:210710354;T:244895308;N:4100", 49, 0, null, null, 243198380, 215821497, 210710354, 244895308, 4100, "SRX2677113", "SRS2075534", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89876, null, 0.11007, null, 0.69467, null, 0.47115, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42087, "SRR5381997", "SRX2677112", "SRS2075533", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 1", "GSM2551989", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 1", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551989", "GSM2551989: ZDR 1 mpf eyes 1; Danio rerio; RNA Seq", "GSM2551989", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551989", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L4_HKZEBxagRAAARAAPEI-201_1.fq.gz", "fastq", 786951466.0, 16060234.0, "GSM2551989 r1", "0:49 1:0", "A:206839376;C:187666900;G:181310367;T:209045476;N:2089347", 49, 0, null, null, 206839376, 187666900, 181310367, 209045476, 2089347, "SRX2677112", "SRS2075533", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89138, null, 0.10868, null, 0.68943, null, 0.45278, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [42088, "SRR5381998", "SRX2677112", "SRS2075533", "SRP102601", "PRJNA380770", "Proteolytic processing of LRP2 on RPE cells regulates BMP activity to control eye size and refractive error", "GSE97125", "Transcriptome Analysis", "We compare dissected ocular tissues from wild type and lrp2 / mutant adult zebrafish in order to examine the genetic pathways underlying the enlarged eye phenotype observed in the absence of Lrp2. ABSTRACT: Mutations in LRP2 a transmembrane receptor cause ocular enlargement and high myopia. LRP2 is expressed by the RPE and eye ciliary epithelia binding many extracellular ligands including Bmp4 and Shh. Signaling mediated by LRP2 is very context dependent and how multiple pathways are coordinated is unknown. Transcriptome analyses of ocular tissues revealed that controlled sustained BMP signaling from the RPE is critical for normal eye growth and emmetropia proper refraction. Using human iPSC derived RPE and zebrafish we demonstrate that BACE sheddase dependent LRP2 cleavage produces a soluble domain that binds BMP4 inhibiting its signaling. We propose that controlled proteolytic cleavage of LRP2 makes two ligand binding receptor forms available: a soluble BMP trap and a membrane bound RPE signaling facilitator. By modulating LRP2 cleavage cells can fine tune and coordinate multiple signaling pathways. This data supports the concept that LRP2 acts as a homeostasis node that buffers and integrates diverse signaling to regulate emmetropic eye growth. Overall design: Examination of whole eyes sclera/choroid RPE and retina in wild type and lrp2 / mutant zebrafish at 1 mpf", null, null, null, "ZDR 1 mpf eyes 1", "GSM2551989", null, "tissue:whole eyes|genotype:wild type|age:1 mpf", "ZDR 1 mpf eyes 1", "Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. \"Dirty\" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz10 GCA 000002035.3 Supplementary files format and content: Excel files containing FKPM values for expression levels.", "whole eyes", null, "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light: 10 h dark lighting cycle and fed a standard diet", "genotype:wild type|age:1 mpf", "GSM2551989", "GSM2551989: ZDR 1 mpf eyes 1; Danio rerio; RNA Seq", "GSM2551989", null, "1", "Eyes were dissected were removed stored overnight at 4C in RNAlater and RNA was harvested using Trizol reagent. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input Illumina protocol.", "GEO Accession:GSM2551989", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP102601", null, null, "150627_I114_FCH2TT2BBXX_L5_HKZEBxagRAAARAAPEI-201_1.fq.gz", "fastq", 914454317.0, 18662333.0, "GSM2551989 r2", "0:49 1:0", "A:240676436;C:218930366;G:211397133;T:243446328;N:4054", 49, 0, null, null, 240676436, 218930366, 211397133, 243446328, 4054, "SRX2677112", "SRS2075533", "SRA549807", "GEO", "Medical College of Wisconsin", 1, 0.89338, null, 0.10969, null, 0.69163, null, 0.46453, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61643, "SRR12899696", "SRX9364743", "SRS7586958", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl R2", "GSM4861209", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf KO", "nrl R2", "Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf KO", "GSM4861209", "GSM4861209: nrl R2; Danio rerio; RNA Seq", "GSM4861209", null, "1", "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861209", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "nrl-R2_combined_R1.fastq.gz nrl-R2_combined_R2.fastq.gz", "fastq fastq", 7231497600.0, 24104992.0, "GSM4861209 r1", "0:150 1:150", "A:1995457626;C:1613822880;G:1630032692;T:1991951852;N:232550", 150, 150, null, null, 1995457626, 1613822880, 1630032692, 1991951852, 232550, "SRX9364743", "SRS7586958", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.91539, 0.91383, 0.13441, 0.13499, 0.69296, 0.70021, 0.5139, 0.50426, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61644, "SRR12899695", "SRX9364742", "SRS7586957", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "nrl R1", "GSM4861208", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf KO", "nrl R1", "Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf KO", "GSM4861208", "GSM4861208: nrl R1; Danio rerio; RNA Seq", "GSM4861208", null, "1", "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861208", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "nrl-R1_combined_R1.fastq.gz nrl-R1_combined_R2.fastq.gz", "fastq fastq", 6989998200.0, 23299994.0, "GSM4861208 r1", "0:150 1:150", "A:1947895730;C:1539849390;G:1551787456;T:1950215842;N:249782", 150, 150, null, null, 1947895730, 1539849390, 1551787456, 1950215842, 249782, "SRX9364742", "SRS7586957", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.90616, 0.9059, 0.15209, 0.15341, 0.68998, 0.69885, 0.49879, 0.49931, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61645, "SRR12899694", "SRX9364741", "SRS7586956", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT R2", "GSM4861207", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf type", "WT R2", "Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf type", "GSM4861207", "GSM4861207: WT R2; Danio rerio; RNA Seq", "GSM4861207", null, "1", "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer's protocol.", "GEO Accession:GSM4861207", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP288615", null, null, "WT-R2_combined_R1.fastq.gz WT-R2_combined_R2.fastq.gz", "fastq fastq", 7066558200.0, 23555194.0, "GSM4861207 r1", "0:150 1:150", "A:1911018201;C:1615965707;G:1630234641;T:1909071420;N:268231", 150, 150, null, null, 1911018201, 1615965707, 1630234641, 1909071420, 268231, "SRX9364741", "SRS7586956", "SRA1147909", "GEO", "College of Life Science and Technology, Huazhong University of Science and Technology", 2, 0.91673, 0.91647, 0.11542, 0.11684, 0.68781, 0.69637, 0.48784, 0.49134, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "sc_generic", "bulk", "bulk", null, "China", "2020-10-26", "Juvenile", "Juvenile", "Eye", "Sensory System"], [61646, "SRR12899693", "SRX9364740", "SRS7586955", "SRP288615", "PRJNA672100", "Nrl dependent and independent rod photoreceptor development in zebrafish [RNA Seq]", "GSE160138", "Transcriptome Analysis", "NRL Neural retina leucine zipper is a key regulator of the fate determination and gene expression of rod photoreceptors in the retina of many vertebrates. In this study we observed a unique retinal phenotype in the nrl knockout zebrafish model characterized by reduced rods with shortened outer segments and gradually increased green cones in maturity. By tracing and comparing the developmental processes of WT and nrl knockout rods we found there might be two waves of rod genesis distinguished as nrl dependent and independent with different starting times. To reveal the underlying cellular and molecular mechanisms bulk and single cell RNA seq were performed. The changes in gene expression and cell proportion of rods and cones agreed well with our histological and immunofluorescence studies. Interestingly we found that rods exhibited noticeable heterogeneities in the gene expression patterns and a part of rods in nrl knockout zebrafish misexpressed the green cone genes reflecting a hybrid status of rod and green cone. Furthermore we identified mafba as a novel regulator of rod genesis which was responsible for the development of rods in nrl knockout zebrafish. Our study will largely improve the current understanding of the developmental processes and regulatory mechanisms of rods in zebrafish and probably other species and may facilitate future studies in the fields of retinal development and retinal degeneration. Overall design: Two WT and two nrl KO samples two biological replicates were analyzed. Each sample represented a pool of RNAs from three zebrafish retinas at the age of 2 month. The differentially expressed genes between WT and nrl KO groups were identified.", "parent bioproject:PRJNA672094", "pubmed:35245286", null, "WT R1", "GSM4861206", null, "source name:Retina|tissue:Retina|strain:AB|age:2 mpf type", "WT R1", "Quality control mapping and expression analysis: Image analysis and base calling were conducted by the HiSeq Control Software HCS + OLB + GAPipeline 1.6 Illumina on the HiSeq instrument. The high quality clean data were generated by Trimmomatic v0.30 and aligned to the reference genome of zebrafish via software Hisat2 v2.0.1. Differential expression analysis: Gene and isoform expression levels were estimated by HTSeq v0.6.1. Differential expression analysis was performed by DESeq Bioconductor package. post adjusted by Benjamini and Hochberg\u2019s approach for controlling the false discovery rate the threshold of p values was set to <0.05 to detect differentially expressed genes. GO and KEGG enrichment analysis: GO TermFinder was used identifying Gene Ontology GO terms that annotate a list of enriched genes with a significant p value less than 0.05. KEGG Kyoto Encyclopedia of Genes and Genomes is a collection of databases dealing with genomes biological pathways diseases drugs and chemical substances http://en.wikipedia.org/wiki/KEGG which was used to enrich significant differential expression gene in KEGG pathways. Genome build: GRCz11 from Ensembl Supplementary files format and content: Tab delimited text files including the raw counts and FPKM values for each Sample Supplementary files format and content: Tab delimited text files showing the foldchanges and p values of the differentially expressed genes", "Retina", null, "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. The preparations of next generation sequencing library were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer\u2019s protocol.", null, "tissue:Retina|strain:AB|age:2 mpf type", "GSM4861206", "GSM4861206: WT R1; Danio rerio; RNA Seq", "GSM4861206", null, "1", "For each RNA sample three eyes lens removed from different zebrafish were homogenized in RNAiso Plus reagent Takara Cat# 9108. Total RNA was extracted following the operation manual. The total RNA samples were quantified and qualified by Agilent 2100 Bioanalyzer Agilent Technologies and NanoDrop Thermo Fisher Scientific. RNA samples with RIN \u22659.5 and A260/280 \u22651.9 were used for RNA seq. 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